Star Trek: Humanity Lost
by Bundo413
Summary: Humanity Lost tells the story of an altercation between the Federation and The Cylons. The latest chapters will deal with Section 31 and events leading up to the events of the first few chapters. Please read, review, and enjoy!
1. Preface

-Star Trek- Humanity Lost 

_Preface_

At the suggestion of a reader the other day, I am re-vamping my current chapter structure. Chapters one through four will now be chapter one, and I will be delivering longer chapters as the story progresses. The following story is a Battlestar Galactica – Star Trek: The Next Generation crossover. As I write, I will do my absolute best to provide necessary backstory as to not keep readers confused and in the dark. As it is, the story takes place from a Star Trek standpoint in the year 2379-2380, which sets it following the events of the movie Star Trek: Nemesis. Also, this story mentions events originally depicted in non-canonical Star Trek novels. Currently, these novels are: Star Trek: Titan "Taking Wing" by Michael A. Martin and Andy Mangels Star Trek: The Next Generation "A Death In Winter" by Michael Jan Friedman These events are only mentioned so that I may help to set the scene of the current goings-on in the TNG timeline. 

As for the Battlestar Galactica timeline, I have decided to set the story before the attacks on the Twelve Colonies depicted in the original Sci-Fi channel mini-series.

_Thank you for taking an interest in my work, and I hope you find it at the least an entertaining story._


	2. Chapter 1

The Cylons were created by humans… 

_They Rebelled…_

_They Evolved…_

_Some are programmed to think they are human…_

_And they have a plan…_

"_The time is 0530 hours_."

Commander Martin Madden stirred before waking, images from his dream still clinging to the edge of his consciousness. He got out of his bed and walked the few feet to his bathroom. Yawning, he tapped the keypad next to the faucet and watched as cold water began to slowly fill the basin. After a moment, he deactivated the stream, and plunged his hands into the water. Flinching slightly at the sudden sensation of cold, he cupped his hands and brought the clear liquid splashing onto his face. The shock from the action did its duty, and he found himself no longer able to remember the nightmare from the previous night.

Madden paused a moment to look at his reflection in the mirror. Staring back at him was a man in his late thirties, with a slightly graying hairline that most of his friends and colleagues said added character. Wrinkles were beginning to form around his eyes and mouth. _Just like my father_, he thought, _I'm growing old before my time_.

The commander continued through his morning routine, a brief trip through the sonic shower, donning a fresh uniform, and trying to comb his unruly mop of hair into some semblance of order. Taking one last look in the mirror, he decided that this was the best things were going to get and finally said, "Time to start another day aboard the _Enterprise_."

Arriving on the bridge, Commander Madden took in the sights and sounds of the first shift bridge crew hard at work. Some were arriving from other turbolifts to relieve the previous duty shift, and Madden basked in how official and professional everyone was being. Currently, the _Enterprise_ was patrolling the Romulan Neutral Zone, which was quickly becoming the hot zone of the decade. In 2379, a Reman named Shinzon had used a thalaron radiation device to liquidate the Romulan Senate and its Praetor, later stepping into that coveted seat himself. The _Enterprise_ was ordered to Romulus to find out what had happened and discovered that Shinzon was not a Reman at all but was in fact a clone of Captain Picard. A terrible battle ensued between the _Enterprise_ and Shinzon's supreme battleship _Scimitar_, finally ending when the android Commander Data detonated a thalaron intermix generator aboard the _Scimitar_, destroying the ship and himself in the process.

Commander Madden traveled to the first officer's station as he recollected more recent events. Following Shinzon's death, a senator named Tal'Aura had risen to power. She had been a member of Shinzon's new order, and many were furious that she had elevated herself to that position. She faced contention from the Romulan military, the newly freed Reman slaves and the Tal'Shiar, the Romulan secret police. While _Enterprise_ was undergoing extensive repairs and overhauls the starship _Titan_ was dispatched to mediate some kind of peace between the factions and so far an uneasy truce was all that was keeping the factions from becoming trigger-happy.

"Captain on the bridge!" a lieutenant at the tactical station called out, interrupting Madden's thoughts. Captain Picard was exiting the port turbolift and heading for his centrally located command chair. "As you were," he said softly, his eyed fixed to the PADD he was carrying. He paused as he reached his command chair but did not sit down. Madden looked up at him and said, "Good morni-"

"Commander, may I see you in my ready room?" Picard said tersely, cutting him off. Without waiting for a reply, Picard turned away from Madden and walked into his small office just off the bridge. Madden was befuddled for a moment but managed to shake it off, rise, and walk towards and through the doors.

"Tea, Earl Grey, Hot," Picard was saying into the wall-mounted food replicator as Madden entered. "Would you care for anything commander?" he asked retrieving his beverage.

"No thank you, sir." He watched as Picard took a sip of the steaming brew and headed to the chair behind his desk.

"Commander, are you familiar with the Gods Favor religious movement?" At first, commander had no idea what he was talking about, but shortly his Academy history classes began to assert themselves

"Oh, of course. They were religious extremists from Earth's 22nd century who thought that humanity was losing touch with its spirituality." Madden was surprised he remembered that particular chapter in Starfleet history.

"They were thought of as little more than terrorists or petty thugs," Picard said. "Eventually, Starfleet found the leaders of the movement but were unable to apprehend them. The extremists commandeered the starship _Alvarez NX-07_ and killed the crew before disappearing into deep space. At the time, tensions with the Romulans were coming to a head and Starfleet was unable to send a search team." Picard took that moment to slide the PADD to Madden. The commander slowly picked it up and studied the display.

From what he new of 22nd century warp ship design, the image depicted on the small screen appeared to depict a starship's warp nacelle, though it was battered and ruptured in many places along its length. Its forward mounted bussard collector was almost completely broken out, and some of the ruptures were so severe as to render the nacelle all but unidentifiable to the untrained eye. Madden glanced up.

"This is from the _Alvarez_?" he asked. Picard nodded.

"It was discovered by the USS _Harris_ during a routine investigation of a star system beyond the edge of charted space. It was immediately towed back to Starfleet Command for analysis, and they have confirmed that it's from the _Alvarez_. The _Enterprise_ has been instructed to proceed at maximum warp to system CN-16 and launch an investigation." Commander Madden's eyes brightened at the news. He had grown weary playing babysitter on the edge of Romulan Space, and now he would be doing what he had longed to do since he first joined Starfleet; explore uncharted space, and maybe solve a two hundred year-old interstellar mystery along the way.

"Commander, re-acquaint yourself with the history of this ship and of the God's Favor extremists. Tell the department heads to do the same. Will schedule a general briefing for 0100 hours."

"Yes, sir. Shall I order the ship to get underway in the meantime?" He noticed Picard's chuckle at his executive officer's unbridled enthusiasm.

"I think that would be for the best, Commander." Madden smiled slightly before Picard said "Dismissed."

* * *

Time Index 000.6732

_Spatial Grid 093_

_Cube 65534-99821_

"_Unidentified vessel detected…engaging assimilation protocols."_

The Borg Cube hurtled through space, closing on its target. The massive star-shaped vessel that was its quarry turned one of its pointed spires toward its aggressor and began to empty its payload of archaic missile-based weaponry. The artillery all but bounced off of the hardened and armored exterior of the Cube ship. In return, the Cube let loose with its vast arsenal of holding and cutting beams. Three of the star-shaped ship's spires were sent careening into the void of space by the shearing forces of the weapons.

In a last attempt at mounting a defense, the star-shaped vessel launched a bevy of assault raiders at the Cube. As the raiders began streaming angrily at the Cube, sections of hull plating opened all across the surface of the cube. From these new openings emerged large rotary gun turrets, and each turret selected a target and let loose with deadly blasts of plasma energy.

From the safety of far off Unicomplex 33A5T-37, the Borg Queen observed the battle. She studied this new species, the way they fought, the armaments they employed, and, perhaps most importantly, the mechanical way they seemed to be fighting. They launched raider after raider at her Cube, never adapting their fighting style. From this, the Queen ascertained that this species had experience in fighting very few other species, perhaps only one other species.

Suddenly, the star-shaped vessel disappeared in an almost blinding flash of light, leaving behind several dozen of the small raiding craft. Immediately, the Queen ordered the Cube to bring them aboard for assimilation. The Cube responded in kind, latching their emerald green tractor beams onto each remaining ship. A majority of the raiders didn't survive the shearing forces and exploded almost instantly, but the Queen was satisfied when she was informed that three of the raiders had been secured.

The Queen felt anxious waiting for the assimilation process to begin, ready to receive the individual minds into her collective. She waited for a few moments…and felt nothing. Angry, she moved her thoughts to the hangar bays on the cube where the raiders were being stored. She was able to see a close up of the ships and saw her drones looking for an access port. The Queen switched to another angle and saw a drone depress a large gelatinous-looking button on the underside of the craft. An access port opened and a gush of viscous liquid drizzled onto the deck of the hangar bay.

The drone that had found the button was studying the vessel's interior so the Queen switched her viewpoint to his. What she beheld intrigued her. The vessel contained no life form. Instead, a large, quivering brain was suspended inside. The Queen looked at the image in awe. This race had discovered the perfect marriage of technology and biology. The Borg Queen issued a new directive.

_Across the vastness of space, thousands of massive metallic shapes moved with a single purpose, a single directive, towards a small section of unexplored space. Their objective was to assimilate anything and everything belonging to Species 9900, or "Cylon"._

Author's Note: This story and its two previous chapters make reference to events depicted in the movie "Star Trek: Nemesis"and the Sci-Fi television series "Battlestar Galactica", as well as the Star Trek books "Titan: Taking Wing" and "A Death In Winter" Captains Log: Stardate 56324.9

* * *

_The _Enterprise _has arrived in the CN-16 system and has begun a general sensor sweep of the area. I cannot help but wonder at the prospect of potentially establishing contact with whomever may have occupied this system following the disappearance of the _Alvarez._ In a few moments my officers will gather in the observation lounge for the mission briefing._

Captain Picard tapped a button on his monitor and it slid smoothly back into his desk. He was appreciative that during the re-fit of the _Enterprise_ following the Ba'ku mission, Starfleet had implemented this design change into all desktop terminals. They certainly helped to free up desk space. Retrieving a pad from the desk he stood, straightened his uniform jacket, and headed onto the bridge.

Picard paused briefly to greet the current duty shift bridge crew before heading through the doors at the back of the bridge that took him to the observation lounge. It was there that Commander Madden, currently seated in the chair that had been until recently occupied by Commander Will Riker, had set up the briefing, and judging from the number of PADD's cluttered around the man, Picard and the officers that were to assemble had quite a bit of data to digest.

Madden stood and greeted Picard as he walked in. Picard nodded in acknowledgement and went to take his usual seat at the head of the table. A few short moments later, the other attendees began to pour in. First to arrive was Commander Geordi LaForge, Picard's chief engineer and the man Picard counted on to keep his ship running for over fifteen years now. Geordi was followed by Commander Worf, who was now on permanent assignment to the _Enterprise_ after he had handed over his duties as ambassador to his son, Alexander. Beverly Crusher, the Chief Medical Officer, arrived shortly after them and took a seat next to Picard. She smiled at him and was handed a PADD by Commander Madden, which she began reading, glancing up at her captain and lover from time to time.

It was only recently that the two had finally admitted their mutual love for each other. Beverly had been languishing in a prison cell on the Romulan colony world of Kevratas and Picard, along with several old crewmates from his early days on the USS _Stargazer_, were assigned to infiltrate the colony and save the doctor. After a brief search, Beverly was located and Picard admitted his attraction for her. Beverly struggled with this revelation for a time, but eventually came to realize that she possessed those same feelings for him. Since that time, they had been romantically involved, though neither of them wished to share this with any of their close personal friends yet.

Picard realized, with only a slight touch of melancholy, that these three were the last remaining officers from his original _Enterprise-D_ crew. Riker and Troi were together on the _Titan_, and Data and Tasha Yar had both perished in the line of duty, Data only recently and Tasha Yar almost fifteen years ago. Picard still felt pangs of sorrow when he thought about the young woman, but for now he pushed the thoughts aside as Commander Madden stood to start his briefing.

"Good morning," he began, taking up his PADD, "as all of you know, we have arrived in star system CN-16, the last recorded location of the starship _Alvarez NX-07_. At the time of its loss, a group of renegades from the God's Favor religious movement were in control of the ship, attempting to evade capture by Starfleet-

God loves you… 

Suddenly, Madden began to feel strange.

There must be some kind of way out of here…

A song? Why would he be hearing a song?

…Joker to the Thief…

Martin dropped the PADD, right before everything went black.

On a large, star-shaped vessel, half a galaxy away, Number Six removed her hands from the tray of bio-neural fluid before her. Her eyes opened as she welcomed him, the one who would be the savior of the Cylons, the one who would deliver them from the cybernetic beings that plagued them.

* * *

In his haze, Martin felt the soft sting of a hypospray as it released its medicine into his bloodstream. As it took affect, Martin blinked his eyes open and glanced around him.

He was in sickbay, lying atop the main diagnostic table. Standing over him was Dr. Crusher, passing a medical tricorder over him. He attempted to rise, but found himself firmly restrained by the biobed's containment force field.

"You stay right there, commander," Crusher said, smiling, "I haven't quite finished here. One minute you were going through the mission briefing, and the next you had collapsed in a heap on the floor. I can't seem to find a medical explanation for it. I'm going to de-activate the containment field, and I'll trust that you won't get up and walk out of here. Understood?"

"Authoritative, isn't she?"

Martin turned his head away from Crusher towards the sound of this new voice. Standing back to Maddens' right stood a tall, voluptuous blonde woman. She wore a long flowing red skirt with a top that left little to the imagination. She was smiling, but to Madden the smile seemed to hide something deeper, some other unreadable emotion. Madden opened his mouth to speak before being silenced by the woman.

"Say 'understood' before she gets suspicious," the woman said, her sinister smile turning to a scowl of impatience and annoyance. Martin felt something click inside his head and without another thought he turned his sight back to Crusher.

"Understood." Crusher smiled and squeezed his arm in a friendly manner before returning to her office on the far side of the medical bay. Once she was out of sight, he immediately turned his gaze back to where the woman had been standing, but found himself staring at a bare bulkhead. He attempted to get off the bed to investigate further, but realized that, against her word, Dr. Crusher had not de-activated the biobed force field. Puzzled, Madden put his head into a more comfortable position and found himself drifting off to sleep. "I must be losing my mind," he said softly before slipping back into unconsciousness.

* * *

Meanwhile, on a star-shaped vessel more than half a galaxy away, Six once again removed her hands from the basin of bio-neural control fluid that flowed like so much water around the large room in which she stood. As her hands left the fluid, they were instantly dried, such was the technology of the Cylons. Six turned to address her waiting colleagues.

"I have successfully made contact with Madden. As soon as he is released from the medical facility, I will begin further operations. We need to re-outline our priorities. We don't know how advanced these particular humans may have advanced over the last two centuries."

Eight-Alpha stepped forward. "The Eights agree. We would recommend sending a basestar if it weren't for the other crisis plaguing us." Six saw the other three nod in agreement, and she too saw the wisdom in Eight-Alpha's words. This Borg Collective was quickly becoming a nuisance. In the span of a few short weeks, dozens of their cubeships had infiltrated Cylon territory and layed waste to cloning facilities, ressurection ships, colony worlds, countless baseships, and thousands of raiders. The Cylons were suffering heavy losses, and everyone in this room was at a loss as to how to bring the carnage to an end.

One of the more senior models stepped forward then, who for some reason preferred to be called by a human name. This one, Leoban, had been around almost longer than any other model present, and he always made sure that the decision-making council knew it.

"We may have to step up progress on Initiative 017." With this simple statement, everyone present knew what he meant. Essentially it meant surrender. Surrendering the Cylon homeworld to the invaders and finding another place to dwell, to wait, to garner their forces and prepare for a retaliatory strike.

"I have a better idea," said another senior, who also preferred being called by his human name, Cavil, "why don't we combine Initiative's 17 and 12?" That immediately piqued Six's interest, and a quick scan of the faces in the room told her that Cavil had the attention of everyone else present. "The Human's will always be a threat, and the last thing we need is to be assaulted on two different fronts. I say we make a pre-emptive strike and wipe out the Twelve Colonies once and for all. We take their planets and colonize them, leave this area of space. The colonies are far enough away that the Borg will probably never find them, as long as we don't leave a trail of clues for them to follow. We know that they have trouble tracking our ships after we make an FTL jump. We need to use that to our advantage. Six, how far along is your operative on their capital planet?" Six was so engrossed in putting the specifics of the plan together in her mind that she didn't realize that Cavil was speaking to her. She snapped back to reality and answered.

"Six-Beta-3 is proceeding as planned. According to her last report, she believes that she can have access to the defense mainframe within the next two weeks." Cavil frowned at this. "Tell her to speed it up. Tell her about the threat her people face. If she continues at her current rate we may not even be here to take advantage of her intelligence." Six nodded in agreement. She then issued orders; who would lead the main assault, who would lead the attacks on the additional colony worlds, who would stay behind and co-ordinate occupational fleets. Once that was done, she turned back to the basin and gently inserted her hands into the fluid. Of course, she had neglected to disclose one bit of potentially vital information. Her contact on the other side of the galaxy…was human.

* * *

_Thank you for reading the latest chapter in my crossover story. I have big plans for this series, so please keep checking in to see the latest updates. Once I have a little more of my time back I hope to be updating at least once a week. And please keep reviewing!! Your feedback is very important to me!_

_-Bundo_


	3. Chapter 2a Interrogation

Time Index 002.4520 

_Spatial Grid 112_

_Diamond-Prime 00015-00125_

The Borg Queen was thoughtful as she observed the specimen lying on the table before her. On the surface, and even somewhat below the surface, this specimen was a perfect example of species 5618. The facial features, skeletal structure, musculature, everything. Just recently though, her drones had discovered something unique below the inner tissue layer. The Queen held this discovery in her hand as she observed the specimen writhing in pain from its recent and unpleasant extraction. To the Queen, it appeared to be a data access port, though an examination of the device had shown it to be extremely archaic. This was why she was standing in this chamber now. She wanted answers.

The Queen instructed her drones to administer a painkiller to the specimen as she approached the table. Her drones complied, and the specimen quickly relaxed.

"You are human." The Queen said simply. The man on the table turned towards the sound of the voice. He gasped as he saw the Queen, as many species had in the past.

"N-no," he stammered. The Queen frowned, angered yet intrigued by his statement. The vessels that the Collective had been destroying and assimilating definitely did not match any known human configuration, and the Queen knew that species 5618 didn't command an army of robotic centurions. Now, someone who seemed to be so inherently human was telling her that he wasn't. This was becoming a most interesting operation.

"Then what are you?" the Queen queried.

"Me first," said the man, "what are you?" The Queen's anger deepened at this beings impudence, but she decided to humor him.

"We are the Borg," she said, allowing a smile to creep onto her face. She watched as the being stared in confusion. It was not uncommon for a species to have no knowledge of the Collective, but it disappointed the Queen when the Borg's reputation did not precede them.

" What is a Borg?" the man asked. As if by answer, a drone stepped up to the diagnostic table. The Queen knew that two-of-eleven was only checking the table's diagnostic readout, but his timing couldn't have been more perfect. The man reacted to the drones sudden appearance as the Queen suspected he would by trying to get as far from it as possible. The restraints affixed to his limbs and torso, however, assured that escape would not be a possibility.

"We bring order to chaos," the Queen said, by way of elaboration. The man was still confused.

"How do you accomplish this?" he queried. The Queen was tired of this line of questioning, and though she realized that she could obtain all the information she required through simple assimilation, she sometimes preferred to interrogate members of newly conquered species in a traditional manner. The Queen found that a species was more submissive if she put a more gentle face on what was happening to them. Resistance, after all, _was_ futile.

"All will soon be revealed to you," the Queen remarked, sidestepping the question. "What do you call yourself?" she demanded, trying to bring the interrogation back on track.

"I am Leoban," the man responded. "Is that your species or your designation?" the Queen asked in return.

"That is my name, my designation as you call it. My species is called Cylon." The Queen smiled. She walked up to the side of the diagnostic table and keyed in a sequence on the control pad. The table tilted up vertically, bringing Leoban eye to eye with the Queen. She held up an arm, and watched as Leoban gasped in horror when two assimilation tubules shot out from between her knuckles and dug into his neck. His eyes widened in fear as nanoprobes began to swim freely through his bloodstream. Finally, Leoban's neck went limp and he moaned in pain.

"You're new designation is first-of-eight," the Queen commanded as the tubules withdrew back into her body. She ran her hand along Leoban's jaw line, tracing it slowly and sensuously, feeling the formation of the cybernetic implants introduced by the nanoprobe injection below his skin. Finally, she brought her lips close to Leoban's left ear and whispered, "You will make an excellent drone."

Well, the plot thickens! Sorry for the brevity of this chapter, this past week has been quite busy. The next part of this chapter will be up in a couple of days, so stay tuned!


	4. Chapter 2b: Anomaly

_

* * *

__April 5th__, 2163_

_Star System CN-16_

_USS Alvarez_

_It is fitting that I record this log on the centennial anniversary of mankind's "historic" warp-speed flight. My, even after all these years those words still stir the bile within me. There was nothing historic about it! It marked the death of humanity's love of God and the goodness and righteousness that he stood for. Ever since, we as a culture have become more dependent on these new "technologies" in our daily lives. Each time we make a so called advance, I feel and my followers feel that we lose a part of what makes us human, we lose what we worked so hard to gain through centuries of spiritual progress. The nuclear holocaust of Word War III has been so easily forgotten by many of my fellow humans, well, it certainly hasn't been forgotten by me. It was a warning from God even then that we as a species needed to renounce our unholy ways and return to his Glory. Over a century later, his warnings still fall on deaf ears. Even as the hated Xindi attacked our planet, we still depended on technology and a starship full of heathens to resolve the crisis._

_Which brings me to the Enterprise, an unsuitable name for an abomination. A vessel that cruises the stars, looking for "new life and new civilizations," and finding only alien species who wish to dilute our once great culture, species with heretical thoughts about God and religion as a whole. If I have my way, Earth will be rid of all of them. I have captured this starship and will use it as my tool to bring the heathens and heretics to light. God will punish them for their sins, and I will be at his side to watch as he delivers unto them his divine vengeance._

_My followers are more capable at piloting this monstrosity than I am. I ordered them to point it towards the center of the galaxy and proceed at its top speed. The God's Favor followers will find God, and we will return to Earth with a force so powerful that nothing, not even an entire fleet of starships will be able to stand in its way. End log._

As Paxton West finished recording the log, he took a moment to say a silent prayer for those whom he and his followers had killed in order to take this vessel. Granted, they were the very heretics the God's Favor movement was fighting against, but Paxton had some room in his heart to forgive them their trespasses. He was sure God would feel the same once they had found him. Paxton wanted only to return humanity to a better time, a time when technology was not a governing factor in their lives. As for the aliens, Paxton knew that God would have no room in his heart for them.

"Your Holiness?" The voice of the movements' High Augur Lynn Dixon filled the captain's office. Apparently she had figured out how to operate the vessels internal communications system. Paxton stood from his seat behind the captain's desk and walked over to the comm. panel near the door.

"Yes, High Augur?" he said, depressing a button to speak.

"Sensors have detected a spatial anomaly just under a light year away. If we continue along our present course we will pass through it in three hours," she reported.

"Have we determined if it is dangerous or not?" Paxton asked.

"Unknown. What are your orders, your Holiness?"

Paxton had a sudden urge. Something deep within his being told him to investigate this phenomenon. He didn't know what it could be, but knew somehow that it was related to God.

"Continue along our present course. We will investigate this anomaly. I'll be on the bridge shortly.

* * *

The bridge of the _Enterprise-E_ bustled with the activity of dozens of crewmembers, each doing his or her part to keep the Federation's flagship running in top form. At the center of it all sat Jean-Luc Picard, captain of the vessel for the past seven years. At this moment, the gaze of most of the people occupying the bridge was turned towards the viewscreen, upon which was displayed a massive spatial anomaly. 

The _Enterprise_ had been sweeping the CN-16 system for a few days now, and had just discovered the decaying remains of some sort of propulsion trail. Picard had concurred with Chief engineer LaForge that it most definitely wasn't a warp trail. Indeed, it didn't match _any_ known propulsion configuration. Picard had decided to follow it, and now they were here, staring into the gaping, churning maw of a never-before-encountered spatial anomaly.

"Analysis," Picard asked Worf, the acting first officer. Madden was still in sickbay after his episode during the briefing a few days ago. According to Dr. Crusher he was medically fine, but she wasn't ready to release him until she had found out what had caused him to faint.

"Despite a threatening outward appearance, the anomaly doesn't appear to be a danger to the ship. There are standard particles that make up most anomalies, however there does seem to be multiple high concentrations of neutrino particles towards the center of the anomaly." Picard thought for a moment. He had read a report recently that mentioned an anomaly spotted with high concentrations of neutrino particles, but for the life of him he couldn't remember what else that report had contained or who had authored it.

"Mr. Fralax," Picard said, turning towards the science station situated behind and to the right of his command chair, "prepare a class nine probe. I'd like to get a closer look at what's inside." Fralax nodded in response and Picard swiveled back toward the view screen. Something didn't feel right about this, and he was determined to find out what.

* * *

"Martin." 

It was that voice again, so sweet and sultry, yet so authoritative.

"Wake up."

Martin Madden's eyes shot open and he found himself staring at the blonde woman he had seen briefly in sickbay. As he looked around though, he didn't seem to be in sickbay anymore. He was standing in his spartan quarters on the _Enterprise_, and the blonde woman was seated on the edge of his bed.

"Who are you?" The woman chuckled, then said, "names have little importance where I come from. But, for the lack of a better label, you may call me Six." She smiled at Madden, then stood up. Martin let his gaze run over her, her beauty captivating him. After a moment though, his Starfleet training re-asserted itself.

"Why are you here?" he asked, as authoritatively as he could. Six only laughed lightly as she walked towards him. She began to circle him, letting her hand trace his shoulders as she went.

"I am here," she began, stopping behind Madden and interlocking her arms around his chest, "to find a long-lost member of my family." Madden tensed at the contact. It had been a long time since he had felt this way, not since-

"What exactly does that mean?" he asked, once again refusing to let her get the better of him. Though he couldn't see her face, he could hear the frown in her voice when she spoke again.

"I have come a long way, Martin. Let's not let this reunion turn sour." Suddenly, he felt her hands grasp his head. A flood of images followed, images Martin had never seen before. "Remember what you are, Madden. Remember, and embrace your identity." Six spoke with an urgency that Martin had never observed in her before. She had always been so in-control, so commanding. Now she seemed desperate, frantic, as if something somewhere had happened and only she knew about it.

The images came faster and faster now. So fast that Martin was unable to discern between them. One that stood out from the rest contained five figures, each wearing an ivory robe and bathed in columns of white light. Another image singled out the central figure, only this time Martin could see his face.

"No, how can this be?" he heard himself scream.

"Remember!!"

Martin tried to block out the vision, but failed. Somehow it was true; somehow, he was staring at himself.

* * *

"Blood pressure is dropping," cried an alarmed Nurse Alyssa Ogawa, "we're losing him!" The cry caused Dr. Crusher to dash from her office towards the central diagnostic biobed, grabbing a tray of medical tools as she went. She arrived at Madden's side just as his heart stopped beating. 

Slapping her comm. badge she said, "Crusher to bridge, commander Madden has gone in to complete cardiac failure. We are attempting to stabilize. I will update you when I can, Crusher out." Crusher grabbed a laser scalpel. She would get this heart pumping again, even if she had to do it with her bare hands.

* * *

Picard had just been about to leave the bridge for sickbay in response to Beverly's call when Worf called to him from the tactical station. 

"Captain, I am picking up several new contacts on sensors. Unknown configurations."

"On screen, Mr. Worf." Picard said, quickly returning to his center chair. Beverly would have to wait. The view screen shimmered to life, now depicting three alien ships against the backdrop of the anomaly. Two of the vessels were almost star-shaped; two modules mounted atop one another each with their own long pointed projections. The other ship however, almost resembled a human ribcage, with spider-like projections running along a large central core. Picard marveled at the design, until he saw the two star-shaped ships unleash what appeared to be a payload of missiles.

"Evasive maneuvers!" he called out. Despite the inertial dampeners, he felt the ship lurch slightly as it tried to get out of the way. "Hail them, tell them we mean no harm," he ordered.

"No response," Worf reported, "their comm. system is not operating on any known frequency. Recommend offensive action." Picard had to concur with his officer. He had to defend the ship.

"Mr. Worf, target the lead ship with a brace of quantum torpedoes. Try to hit them at that connecting point between the two modules." Picard hoped that that was a weakness of the ship.

"Captain," now it was Fralax who was speaking, "I am picking up dozens of other contacts, all small fighters heading this way. They're firing!" Picard waited for the ship to be buffeted by dozens of ships firing in tandem, but it never happened.

"Mr. Worf, fire. Mr. Fralax, find out what we were hit with." Picard watched as several of the bright cerulean quantum torpedoes went cruising out towards the large lead ship. He watched as they impacted the central core, and he watched as the ship was torn into two parts by the resulting explosions. Chain reaction explosions began to tear their way through the rest of the ship, before finally there was nothing left but debris. The view screen also showed the fighters that had been "attacking" the _Enterprise_ flying back towards the debris field.

"Jarax, give me an analysis of-," Picard was unable to finish before two blinding flashes of light filled the view screen. When Picard looked again, all of the ships were gone.

"Captain," came Dr. Crusher's voice through Picard's communicator, "I did everything I could, but I regret to inform you that Commander Madden has just died."

* * *

Darkness. 

Then, Madden felt a hand holding his. He heard voices.

"Breathe through it, breathe through the pain." The voices sounded like a disjointed chorus, and he wondered what was muffling them so.

Then he felt the fluid, encasing his body like a cocoon.

Finally his eyes opened. He was lying in a pool of some kind of viscous substance. Surrounding him were half a dozen people, people he had seen before but he couldn't remember from where. From the back of the crowd emerged Six, though something seemed different about her. She seemed more…real. She knelt down beside the tub and stroked Madden's hair, slick from the fluid in the tub.

"Welcome back to us," she whispered, "number 13."

_This was the last part of chapter 2; I hope you enjoyed reading it as much as I enjoyed writing it. Chapter 3 will be coming in another week or so, so keep checking the site. Sorry to leave you with a cliffhanger here…well, not _too_ sorry. Whether you're enjoying this story or not, leave a review and let me know. Your feedback keeps me going._


	5. Chapter 3: Section 31

_Location Unknown_

_One year after the conclusion of the Dominion War_

The jungle clearing was coated in a dense morning fog, and Cole was having a hard time seeing even five feet in front of him. This was proof that he was getting complacent in his old age. Hell, even just four years ago he wouldn't have agreed to meet a completely unknown individual at equally mysterious coordinates. Well, in truth Cole knew the coordinates very well. He just didn't wish to share that information with his mysterious host. He still didn't know why he had agreed to meet on Sindorin of all places, but something about the stranger's voice had compelled him to comply.

The only thing Cole knew about the planet Sindorin was that it had up until recently been a hatching facility for an advanced breed of Jem'Hadar soldier, conditioned to serve Starfleet instead of the Founders. It was a shame that the project, like so many other Section 31 ventures lately, had failed miserably. Fortunately, Cole had been able to shut the lid on the whole thing. That still didn't do much for his reputation within the organization. Sindorin and Ethan Locken had been his responsibility, but once Locken had gone rogue, Cole had had no choice but to liquidate him.

It was interesting, he pondered, that the recent failed Son'a-Bak'u venture had been his project as well, and that operation had ended, as the phrase would describe it, "shit side up". Cole usually didn't like using such colorful metaphors, but in that instance it was the only one that fit. Dougherty had assumed too much control, believing that he was truly acting in the best interests of the Federation. He had gone rogue, but before S31 had a chance to liquidate him, Ru'afo did it for them. Cole had never had the pleasure of a Son'a flesh stretching device before, but he imagined that on the right setting it could prove particularly painful.

A rustling in the bushes ahead of him, at least the ones he could make out, sent Cole's hand flying to the phaser attached to his belt. He took careful aim at the source of the noise and called, "if you don't show yourself in the next two seconds I'm going to cause the largest forest fire Sindorin has ever seen."

"Actually, Mr. Cole, the destruction of the Dominion hatchery is the largest fire Sindorin has ever weathered."

Cole paused. The voice seemed familiar, but he couldn't place it. When the man stepped beyond the confines of the bush though, he realized he didn't have to. Luther Sloan was standing before him.

"If memory serves me, you're dead," said Cole, tightening his grip on his phaser. The man who appeared to be Sloan only smiled.

"Actually that was only one of the many Sloan models," he responded. It was then that Cole heard the clomping sounds headed towards them. It sounded like footsteps, only extremely heavy and even more unnatural. Cole dared not move, for he saw the threatening-looking weapon strapped to "Sloan's" waist, and he didn't think that at his age and physical condition that he would be able to escape before "Sloan" shot him.

Finally, the clomping sounds gave way to a clomping sight. Out of the large bush that served to border "Sloan" emerged two robotic creatures. They both stood about seven feet tall, were heavily armored, and sported lethal-looking gun emplacements at the ends of their skeletal arms. Instead of eyes, a red scanner panned back and forth across the creatures "skulls", emitting a low, ominous hum with each pass. Cole immediately recognized these creatures from the classified reports.

"We had wondered when the Cylon's were going to show up."


	6. Chapter 3b: Section 31 part II

_**The planet Sindorin**_

_**One year after the conclusion of the Dominion War**_

_From the previous chapter:_

Finally, the clomping sounds gave way to a clomping sight. Out of the large bush that served to border "Sloan" emerged two robotic creatures. They both stood about seven feet tall, were heavily armored, and sported lethal-looking gun emplacements at the ends of their skeletal arms. Instead of eyes, a red scanner panned back and forth across the creatures "skulls", emitting a low, ominous hum with each pass. Cole immediately recognized these creatures from the classified reports.

"We had wondered when the Cylon's were going to show up."

"Sloan" only smiled in response. The Cylon centurions that flanked him stepped forward, towards Cole. In response to the hostile maneuver, Cole centered the sights of his weapon on the closest centurion and fired. The metallic monstrosity disappeared in a bright shimmer of light, leaving no evidence that it had ever existed. That was why Cole preferred the S31 model phaser. Kill _really_ meant kill.

Without wasting a beat, the other centurion raised its arm to fire, but Cole was faster, squeezing off a shot before the centurion could even fire. As the creature disappeared into oblivion, Cole re-centered his aim on the doppelganger "Sloan". "What's your model number, hmm? Twelve? Seven?" "Sloan" only laughed, having not flinched during Cole's destructive outburst only seconds before.

"I don't have a number. This assignment isn't being sanctioned by the Cylon Command. The five of us are doing this all on our own." With that, "Sloan" produced a PADD and tossed it at Cole's feet. Cole bent to pick it up. On it was displayed four names:

_Rear Admiral Matthew Dougherty_

_Ensign Elussar Dalmorivik_

_Section 31 Agent Luther Sloan_

_Lieutenant Commander Martin Madden_

"These are the infiltrators?" Cole queried. "Sloan" simply nodded. "Why are you delivering this information. You do realize that we'll immediately incarcerate these people." "Sloan" smiled again. "We aren't worried about our people." Cole was though. The fact that the Cylon weren't worried about their own operatives could mean many things, and Cole knew that "Sloan" wouldn't be sharing anything else with him.

"How many other centurions are out there?" he asked. "There are none. This meeting was a simple exercise in strategy. We now know that the Federation possesses weaponry capable of utterly destroying us. We also know that you are aware of our existence and have been for some time. The only thing you know are the names of four of our five operatives in the Alpha Quadrant. I believe that we have you at a disadvantage. I will not prevent you from reaching your shuttlecraft, or from leaving this place, or from reporting back to your superiors. Good day, agent." With that, "Sloan" stepped backward into the bush from whence he had emerged and disappeared into the endless jungle expanse that bordered the small clearing in which Cole had just had one of his most peculiar meetings.

As Cole turned to leave, two bright columns of light appeared and flanked either side of him. Two people materialized and immediately began advancing towards him. Cole attempted to defend himself, but as he parried an attack by one man the other pressed a hypospray to his neck. Cole fell limply into the arms of his assailant.

"Let's get him back to the Runabout," said Commander Elias Vaughn.


End file.
